CHE.496/2008/Projects/2/Group 2

Group 2's project overview and part design

List of initial ideas

• Foundational
  • Parts for genetic circuits
    • New light sensor (i.e., new wavelength)
  • New chassis (e.g., yeast)
    • Standardized plasmids
    • Standardized restriction sites
  • Optimizing existing parts (e.g., inverter)
  • Compartmentalization/insulation
    • Molecular screens (filters) that enable signal isolation and insulation (inside the cells and in between cells)

• Computational
  • modeling of biotech-relevant microorganisms

• Synthetic Biology Tools
  • Quality characterization techniques
  • Ways to insulate biological signals

• Genetic Circuit Engineering
  • Light-based repressilator
  • Light switch

• Biosensing
  • Ethylene biosensor
  • Algae that sense light and displays permanent memory

• Metabolic Engineering
  • Polysaccharide synthesis (for food)
  • Bioplastic production
  • Chemical degradation (toxin breakdown)
    • Oil
    • CO2
    • Plastics

List of top two project ideas

• Biological production of plastic
  • Polyhydroxyalkanoates (PHAs) are naturally synthesized polyesters in Ralstonia eutropha
  • These PHAs are used for energy storage
  • Polyhydroxybutyrate (PHB) is a PHA and could possible replace polypropylene
  • Biologically-produced plastics represent a sustainable chemical industry that is not dependent on petroleum
  • Three genes necessary for PHB synthesis: phaA, phaB and phaC (from Pohlmann et al., 2006)
  • Pathway: 2 acetyl-CoA are condensed into acetoacetyl-CoA by phaA. Then, phaB (NADPH-dependent) reduces this to (R)-3-hydroxybutyryl-CoA. Finally, this is polymerized into PHB by phaC.
  • phaA (code for acetyl-CoA acetyltransferase) Nucleotide sequence
  • Possible use in tissue engineering applications (PHB is found in blood plasma)
  • Chassis: E. coli
• Biological degradation of plastic
  • Biodegradation of natural plastics
    • PHAs are biodegradable.
  • Biodegradation of synthetic plastics
    • Streptomyces, a gram-positive bacteria, can naturally break down polyethylene
    • Phanerochaete chrysosporium manganese peroxidase breaks down polyethylene [http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nuccore&qty=1&c_start=1&list_uids=155203612&uids=&dopt=fasta&dispmax=5&sendto=&fmt_mask=0&from=begin&to=end&extrafeatpresent=1&ef_CDD=8&ef_MGC=16&ef_HPRD=32&ef_STS=64&ef_tRNA=128&ef_microRNA=256&ef_Exon=512 dflkjsdlkfj